The preference affects each Watcher, not the connections to the server over all the Watchers and FTP Browser windows open at the time. So in your case, each Watcher is limited to one connection.
One way to get around this would be to use several frequently scheduled synchronizations working off one Bookmark. Not quite the same solution, but the closest you'll get with this limitation on the server.
The only other way is to get your server admin to allow several connections - preferably more than the number of Watchers you intend to use.